Research workbench
Crystal structure of the SAM-SAH riboswitch with SAM from space group P312
Analyse Crystal structure of the SAM-SAH riboswitch with SAM from space group P312 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YMM
- Type
- RNA
- Length
- 70 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Molecule
- Chains: A; Chains: B,D
- Ligands
- SAM, NA
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Chains: A | rna | 26 | — | — |
| B, D | Chains: B,D | rna | 9 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.47 | 0.76 | 14 | SAM |
| 2 | 186 | 0.45 | 0.75 | 13 | SAM |
Interfaces
3 interfaces between chains.
- C–D · 487 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- A–B · 405 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- A–C · 192 Ų buried · 7 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6YMM · Crystal structure of the SAM-sah riboswitch with SAM from space group P312 · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6YMM · PDBe 6YMM
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